Naruto of the Roots
by NaruShika-Forever
Summary: Naruto is taken into the root program at the age of 4. The Hokage knows that he is with Danzo but is convinced Naruto still has all his emotions. How can someone act so well while being so emotionless? How is he worse than Sai? Root!Naruto. Powerful!Naruto Rating may go up.
1. Chapter 1

Sorry I'm so fucking lazy. Like, really. I should have been able to complete a few chapters of some stories but instead just read... hehe. Oh, I've also started a _Holly Naruto _fic , a Naruto hunter x hunter fic (which is now up), one where Naruto is kinda like that zombie fungus and can take over peoples minds, a dark Naruto, and Insane Naruto, _Naruto, son of the Kyuubi, _A naruto one piece crossover, and a few others. I've also started a story with one of my friends, but it's not a fanfic... hehe. Sorry.

Other news about my pathetic life... um... I saw my cousins from California and they were here for about a week! So that was less typing time... huh... whatever. I went shopping! Like, cloths shoping and I actually found stuff I like! That's almost never happened before! And I saw my cousin who came back from collage for a bit! She's going to go back soon, but what ever.

Have any of you seen that new anime about bread? _Yakitate! Japan_. It's hilarious!

Anyways, on with the story!

* * *

"Find him!" A shinobi screamed at his comrades as they searched through the whole of Konoha. A young boy the age of four went missing just hours ago. All the ninja in the village have been searching desperately for the young boy because of the command of their Hokage. In truth, not many were looking very hard. Only just enough that they couldn't get blamed for not helping. Why is this and why would anyone go through so much trouble, just to find a four year old? Well, this is no ordinary little boy. This is a jinchuuriki. A human sacrifice. His name? It's Uzumaki Naruto. Remember it.

"Where the hell is that little demon? Ugh, making us go through all this shit." A different one said to his friend softly. The man next to him shrugged.

"I don't care. Let's get this over with."

As all this was happening, a man was talking with Naruto. Well, talking can't actually be the word for it. It's more like brain washing.

"They all hate you. Even your precious Jiji. Everyone believes you to be a demon. Do you want to know why, little one? Because you're a jinchuuriki. A human sacrifice. And a powerful weapon that they fear. Do you know what fear turns into? Hate. Do you see the problem here? Emotions destroy. People need to just seal up their emotions in a cage. Now, wouldn't the world be so peaceful like that?" He got a hesitant nod in response. It was just enough to make him smile. He was successfully creating a weapon for Konoha. "Good. Now, what should people do to being peace?"

"...Get rid of their emotions?" Danzo frowned. The boy might have the main idea, but he said it like a question. That won't work.

"Yes, so what should you do?" Naruto paused, thinking.

"I don't know. What do demons do to bring peace?" Danzo stared for a moment before talking again.

"Naruto, the civilians were wrong. You aren't a demon. Remember what I said about them fearing you? That's why they say you are a demon. Naruto, you are a human with to many emotions. Now, what should you do."

"Get rid of my emotions. All of them." He said. The smile on Danzo's face came back.

"Good. Work on that." He said just before leaving the holding room. 'This boy will become great after I finally get rid of all the unneeded feelings. He just might become my greatest.'

One week later

"Hiruzen. I found the jinchuuriki brat." Danzo said as he walked into the Hokage office. The worn out old Hokage looked up hopefully. It was then he noticed the little blond boy standing behind his rival. The little boy seemed a little... broken. The Sarutobi felt anger filing him at the thought of what someone must have done to such a young boy.

"Who?"

"A group of villagers. All of them are now dead. And Naruto now knows about the kyuubi." Danzo let Hiruzen think this through before speaking again. He had some guilt tripping to do. "You should have just let me take care of him. I told you this would happen, but you didn't listen. Now look at him. His little mind is broken. But I can fix it. Let him stay with me for a month. You can come and make sure I'm not doing anything. You'll see that he will still have emotions. Even if he didn't, it would be better than what he went through. You wouldn't believe what they did to a poor little 4 year old." The Hokage's head fell into the desk. He was too ashamed of himself to look at the little blond.

"Stop. I'll let you take care of him. But, if I even think you're doing something, I'll take him back. Got that?" He said, a fierce look filing his once sorrow filled eyes. Danzo almost let a smirk lift his lips but stopped it just in time.

"I expected nothing more Hiruzen." He said before turning with a flutter of his robe. He walks until he reaches the doorway before turning a little. Naruto didn't follow him. Instead the blond was hugging the Sarutobi and crying silently. Danzo only had to wait a moment before Naruto let go and began to follow him out.

Once outside the Hokage tower and halfway to the root base Danzo began talking quietly to Naruto.

"Good job boy. He believed you." Naruto nodded slightly to show that he heard, his eyes going blank for a second before going back to the look off a fearful child. Danzo remembered what he told the boy just before leaving the root compound through a tunnel leading to the other side of Konoha.

_"Naruto, do you remember what fear felt like?" Danzo asked._

_"No." Naruto said with a blank look in his eyes. After an intense week of training the boy out of his emotions, Danzo had almost completely succeeded. It was easier for this boy than the others- most likely because of his lack of connections and people to interact with that would show him the better emotions like happiness- and only took a little over a week. The only problem was finishing something he thought would be better than just keeping the boy hidden. He now had to convince the Hokage that it was best if Naruto stayed with him, Danzo. And to do that he needed Naruto to become a little actor._

_"I want you to try and remember the feeling, but don't actually let it out. Try." Danzo commanded. Naruto thought for a minute before life filled his eyes and a look of great pain contorted his face._

_"Perfect."_

Oh yes, Naruto would be the greatest root operative ever.

* * *

How was it? Love it? Hate it? I know that it was short, but _REVIEW_! And **look at my poll! **I'm actually really exited! A whole 19 people have looked at my poll! That's amazing!


	2. Chapter 2

Okay, this is pretty amazing! Brother of a magician has 102 followers! and 77 people have voted on my poll! Isn't that just awesome? Thanks everyone!

Normal text

"Speaking"

'Thinking'

* * *

Chap. 2

_Operation Initiate Into Society is a go._

"Naruto, what are the rules?" Danzo asked before taking Naruto out ROOT's compound. They were standing in front of the steal door front enterence/exit as Danzo tested Naruto about what he was supposed to do.

"Smile, look happy, be friendly, don't talk about training, agree with everyone." He said, forcing his face into a natural looking smile that has his eyes twinkling with it.

"Good." Danzo led Naruto out the door and to the playground to meet the other kids his age and convince Sarutobi that he wasn't taking Danzo's training.

People on the street kept looking at Naruto with nearly concealed anger, something Naruto, if he had been normal still, should have reacted to. But he kept smiling.

That's where Danzo saw his first problem. Naruto didn't change his facial expression, not once. He drew his charge to the side of the road and told him to feel the energies in the air.

"There's a small amount of KI, is that what you mean?" He asked, face shifting into a look of curiosity. It was perfect. You could even see the twinkle in his eyes, that little spark that anyone with a childlike mind has. A mind he had gotten rid of but was able to mimic perfectly. Now, if only he could show fear…

"It's the expression of 'fear' that you have to show. I'll have to instruct you on it later. For now, just stay behind me and pretend to hide from everyone. Understand?" Danzo said, leaving no room for disagreement. Not that Naruto would, anyways. Of course, that also meant Naruto didn't feel the need to answer. "Now, let's go." And they walked back to the busy streets.

"It's the demon brat!"

"Why isn't that thing dead yet?"

"Shouldn't have been created."

"Look, it's being protected."

"No, he's protecting us from it."

With each comment, Naruto stood closer to Danzo, successfully making everyone think he's scared like a normal child would be.

...Progress.

And then they arrived at the park.

"It's time to play, Naruto. Go to kids your age and remember your job." Danzo said in his normal cold voice. Naruto answered with a quick 'Hai' before walking off to play with the kids, slowly adding energy into his step as he went until he was basically bouncing as he walked. Danzo nodded in approval before leaving Naruto to his mission.

"Kiba, go on. Play!" Tsume said, prying her son off of her.

"NOOO! BACK HOME!" He screams. Last time he went to 'play', his sister started throwing weapons at him. It wasn't his fault! Really! How was he, a seven year old, supposed to know not to touch a girl there! It just wasn't fair! And who cares if she was scolded for it afterwards! That scared his little mind!

However, Tsume had no sympathy for her little pup.

"GO!" She shouted, scaring him more then the thought of getting chased by his sister again. He quickly dropped her leg and ran off to the trees.

'Girls are scary… is that what cooties do?' Kiba thought as he ran. 'Must be. Only girls have cooties.' He decided.

And then he crashed into something.

"OOOWW!" Kiba yelled, tears filling his eyes. The boy in front of him blinked, looking down at him. He was completely unaffected by the crash.

And then he pouted and began to cry, the tears falling in slow motion down his cheeks and to the ground. He let out a little whimper before dropping to the ground himself, holding his arm - what Kiba crashed into - close to his side. Kiba automatically stopped his tears, moving to help the younger-looking boy.

"I'm sorry." He said. Naruto looked up at him with teary eyes.

"I-It's fine." He said with a shaky voice. Kiba couldn't think of a good way to apologize accept -

"Do you want to play wit' me and my friends?" Naruto's eyes brightened up and he wiped the wetness from his eyes.

"Can I? Really?" Kiba nodded, causing Naruto to grin in happiness. "Yay!" He cheered. Kiba giggled a little before motioning for Naruto to follow him and running off into the trees. Naruto's smile dropped for half a second and his eyes lost all of their light. This was harder than he thought. But his still has a mission to complete.

With all his features returning to that of an excited little boy, Naruto followed his new little 'friend'.

His mission was going well. Let's just hope it stays that way.

Omake

Danzo got a great idea to make Naruto able to mimic the expression of almost concealed fear. He reached into his pocket, pulled out a book, and showed Naruto one page that was book-marked. On the cover was a little boy cowering away from three shadows. Naruto studied if for a moment before moving his facial muscles into the correct position. Danzo smirked.

"Perfect. Thank god for manga!"

* * *

Ya know what? Screw the length! I can't get it any longer than this! Sorry, 1200 word's my limit. Well, 900 today... but normally 1200!

_**CHECK MY POLL TO SEE WHAT FANFIC YOU COULD GET NEXT! OR TO YELL AT ME FOR NOT GETTING OTHERS DONE! Actually, don't vote on any more. Just yell at me.**_

Oh, and also **review**! I'm actually wanting those lately... weird.


	3. Chapter 3

Special thanks to _kieran aitken_ for writing the fight scene for me! I really can't do what he can. Dude's magic! He's also the reason for the Omake at the end.

Lunarella01827- I don't know what manga, there's too many like that…

Yugioh Luva Girl, Guest, emijonks2000, thank you for your wonderful reviews~

Every one should thank _Taintedangel133_, for she is the reason I have updated to day. And she's my beta, so...

Chap. 3

"Report." Naruto had returned from his first mission. Initiation successful, Naruto befriended all of the group members. After a long discussion of the disease known as cooties, the group went to play on a construction called swings. Naruto could barely fight down his interest in this technology, it was unlike anything he had seen before. The 'seats' moved with minimum effort, far different from the tools in Danzo's training room which take monstrous expels of energy to move. The children around him had been laughing and smiling, and Naruto did his best to mimic their actions with much success.

"The youths accepted my presence without difficulty. I have been asked to join them on a later date, as well as tomorrow at the play area. The progenitors of the Nara have asked me to come to their home after our play." Danzo was pleased. Naruto was turning into a fine boy, able to convince veterans with his acting.

"Good. And what of the Inuzuka's dog?"

"No difficulty. The animal has not developed a sense for emotions as of yet."

"I expect you at the training room at your normal time. 728 will train you today." Naruto nodded curtly and left the room. 728 was the woman who would train him when his normal teacher, 895, was out. 895 had been placed on a mission in a different country, though Naruto didn't know which one. 728 had green hair and sharp features. She had the Kekkei Genkai of the Iburi clan. Her mother had come from the Iburi, her father was a traveler of the world who originated in Mizu. Her kekkei genkai allowed her to turn parts of her body into smoke at will. She was able to force Naruto into more difficult positions by dispersing kill spots that he would normally strike at, and forcing him to create a moment of surprise when she re-materialized.

Naruto left Danzo's chamber, saying nothing when no words of acknowledgment were needed. People in ROOT did what they were expected to do, anything outside the realm of expectation was punished, whether the outcomes were good or bad.

* * *

Naruto arrived in the room, 5 minutes before the decided time as he had been doing for his three weeks of training. And, as per normal, he wasn't the first to enter the room. 728 was facing away from the room's entrance, preparing today's implements for his training, judging by the array of newly sharpened objects strewn around her.

A gentle walk changed into a silent run. Naruto leapt into the the air, drawing a overly sharpened kunai from his sleeve, meant to be plunged into the sea of emerald that flowed from the top of his target's head.

In one swift movement, all Naruto's accumulated force accounted to nothing as his target spun to the right side of him and pushed his arm aside as if he were a speck of dust. Naruto soon found a fist implanted into his abdomen, and, try as he might to hold in any reaction to bodily harm, Naruto coughed up blood as he flew across the room. He hit the wall, but not before he noticed 728 going back to her tools.

Naruto quickly flipped himself to his feet to see 728 leaking smoke once more, though in much larger amounts this time.

No. 728 stood and angled her head sidewards as her body shifted into an astral amalgamation of densely packed smoke. She forced her body to meld through itself, causing her front to now be facing Naruto.

Alas what caused a tinge of fear within Naruto was the implements of his demise held between her fingers. Eight serrated, curved blades made precise for the job of rendering flesh from bone, and causing agonizing pain while doing so. In a matter of seconds all eight blades were hurtling towards him.

Using seconds of precious time, the blonde's mind had the blade's trajectory analysed and calculated. The back three blades travelled further apart than the two lead blades which headed straight for him. To minimize his chances of escape, 728 threw two blades up high to prevent him from vaulting over her onslaught. The last blade was sent low, preventing him from sliding under the attack.

In a fraction of a moment Naruto felt numb. His legs began to move, torso lowered itself nearer the ground. Naruto could feel chakra gathering around him.

None of this was by his choice, only instinct.

The blonde watched from a third person perspective as his body slid beneath the lowest blade. Watching from this perspective, Naruto found his calculation had been off, allowing him more mobility than he had expected.

After passing under the blade, a leg materialized and slammed down onto Naruto's abdomen. Blood spilled from the corner of his mouth, slowing to a drizzle only for more to froth up when a second boot slammed into him.

Smoke began gathering around the legs forming a torso, arms, and an impassive, chiselled face.

"Improve." 728 said, before her boot came crashing down on him once again.

Naruto had to think fast. Quickly substituting himself with one of 728's weapons, Naruto used moments to switch back with the blade and thrust his knee forward. He had seen from a 3rd person POV, and could clearly see the best course of action. In addition, 728 had picked up the weapon and was about to throw it at Naruto.

The emerald locks passed by the woman's face as the wind summoned by the child's kick had pushed them back, much unlike herself.

Instinct coursed through her, her arm in a motion to intercept the attack. What she hadn't expected was for Naruto to turn mid kick and extend his leg so, instead of a knee, it had become a roundhouse kick aimed for her face.

As his foot neared 728's head Naruto felt something on his leg and cast a glance to see a smoky hand on his shin.

Using all of Naruto's strength against him 728 twisted underneath the child and slammed him front first into the ground. 728 then proceeded to take one of the boys arms and pulled it back whilst she had a foot squarely between his shoulder blades to prevent him from rolling away.

"You need to improve, else you die, boy." Came a male voice from a shadow set in the corner of the room. Out stepped a person Naruto had never met before. 728, however, bowed in respect when the man came into view, so Naruto did as well.

"281." 728 greeted. Naruto recognized the number. Danzo had told him all of the important members of their organization, and 281 was one who had the most knowledge of the organization, and would be considered trusted by anyone else's standards.

"I have been asked to take over young Naruto's training when you are done with him." 728 bowed once more before 281 left the room. When his presence had fully disappeared, 728 separated her body parts, sending them flying at Naruto.

And their training continued.

* * *

It was time for Naruto to join the Nara in a game. He and Shikamaru decided on Shogi, Shikamaru promising to teach him how to play. Shikamaru and Shikaku demonstrated by performing a teaching game, introducing Naruto to the basics as well as more difficult strategies.

After the game, Shikaku left the room and allowed the two to play on their own while he went to grab something to eat.

Both of the boys played in silence, not caring to start up a conversation because of their quiet natures. Naruto found the game fairly difficult for his first try, while Shikamaru was trying hard not to fall asleep. Even he knew it wasn't nice to nap while there was a guest over, especially a new friend. Now, if it was Choji, that was a different matter.

"How's… this move?" Naruto asked, genuinely interested. Shikamaru cast a glance at the board and picked up Naruto's recently placed piece.

"Your knight will have a clear shot at my promoted bishop in this case." Naruto carefully studied the gameboard.

"After capturing the bishop, I should be able to have a shot at your king, right?"

"No." Shikamaru corrected, Naruto's face becoming downcast. Shikamaru thought he should try and comfort the beginner, but he had no idea what to do. So, he tried distracting Naruto. "Well, we should probably go get something to eat. Besides, Choji is planning on being here soon and I want food in my stomach before it's gone." It was more than he ever planned on saying in his life, but he didn't like it when people looked like Naruto just did. Completely defeated. That would be the only reason Shikamaru would actually become a ninja by choice. But his mother was already having him go to the academy, so he didn't have that choice in the first case.

Naruto couldn't help but feel… disappointment when Shikamaru gave up on teaching him. Naruto wasn't used to being so bad at something that would just give up anymore. Ever since Danzo had come, he had been making progress and people would continue trying to get him to learn.

"Are you coming?" Shikamaru was standing at the door, waiting for Naruto to at least stand before he started on his way. Naruto nodded, silent. He would have to improve. Shikamaru should not grow bored with him so easily. Naruto would not allow it.

Omake

728's power was getting on Naruto last and only nerve. He had already been fighting her for 2 weeks, and he had yet to land a single hit on her. People who could disappear were impossible to fight, and Naruto was done with it. All of these people can go to hell!

Naruto metaphorically threw down the towel and walked out of the room, silently cursing all of the people who could do this.

XX

Hidden in an underground base, preparing for his future role as the one named 'Tobi', Obito felt a tear welling in his eye.

"T-T-Tobi is a g-g-good boy." He said, wiping away the tear. "Who's mad at Tobi? Tobi doesn't like this…" He muttered to himself before sighing. "This is stupid. Who sounds like this?" Without another word, he disappeared into his dimension, his body becoming intangible before disappearing all together.


End file.
